refactor: use services layer and modularize transfer operations

Decouple CLI commands from internal helper logic and consolidate the
core file transfer operations in the service layer to improve library
portability.

- Make MdrsClient subclass MdrsService to inherit resource resolution.
- Remove all deprecated helper methods from BaseCommand.
- Move core upload and download logic to a new transfer module.
- Refactor all CLI commands to route actions through MdrsClient.
- Eliminate circular imports between client and CLI command modules.

mdrsclient/commands/ls.py

@@ -5,8 +5,8 @@ from typing import Any
 from pydantic.dataclasses import dataclass
 
 from mdrsclient.api import FilesApi, FoldersApi
+from mdrsclient.client import MdrsClient
 from mdrsclient.commands.base import BaseCommand
-from mdrsclient.connection import MDRSConnection
 from mdrsclient.exceptions import UnauthorizedException
 from mdrsclient.models import File, Folder, FolderSimple, Laboratory
 
@@ -19,7 +19,7 @@ class Config:
 @dataclass(config=Config)
 class LsCommandContext:
     prefix: str
-    connection: MDRSConnection
+    client: MdrsClient
     laboratory: Laboratory
     password: str
     is_json: bool
@@ -58,21 +58,27 @@ class LsCommand(BaseCommand):
         from mdrsclient.client import MdrsClient
 
         client = MdrsClient.from_remote(remote)
-        client.ls_command(remote_path, password, is_json, is_recursive, is_quiet)
+        cls._ls_logic(client, remote_path, password, is_json, is_recursive, is_quiet)
         return
 
     @classmethod
     def _ls_logic(
-        cls, connection, remote_path: str, password: str | None, is_json: bool, is_recursive: bool, is_quiet: bool
+        cls,
+        client: MdrsClient,
+        remote_path: str,
+        password: str | None,
+        is_json: bool,
+        is_recursive: bool,
+        is_quiet: bool,
     ) -> None:
         remote = remote_path.split(":", 1)[0] if ":" in remote_path else ""
 
-        folder, laboratory = cls._resolve_folder(connection, remote_path, password)
+        folder, laboratory = client.resolve_folder(remote_path, password)
         laboratory_name = laboratory.name
-        files = cls._find_files(connection, folder.id)
+        files = client.find_files(folder.id)
         context = LsCommandContext(
             f"{remote}:/{laboratory_name}",
-            connection,
+            client,
             laboratory,
             password if password is not None else "",
             is_json,
@@ -102,7 +108,7 @@ class LsCommand(BaseCommand):
         for key in label.keys():
             length[key] = len(label[key]) if not context.is_quiet else 0
         for sub_folder in folder.sub_folders:
-            sub_laboratory = context.connection.laboratories.find_by_id(sub_folder.laboratory_id)
+            sub_laboratory = context.client.connection.laboratories.find_by_id(sub_folder.laboratory_id)
             sub_laboratory_name = sub_laboratory.name if sub_laboratory is not None else "(invalid)"
             length["acl"] = max(length["acl"], len(sub_folder.access_level_name))
             length["laboratory"] = max(length["laboratory"], len(sub_laboratory_name))
@@ -147,12 +153,12 @@ class LsCommand(BaseCommand):
         if context.is_recursive:
             print("")
             for sub_folder in sorted(folder.sub_folders, key=lambda x: x.name):
-                folder_api = FoldersApi(context.connection)
+                folder_api = FoldersApi(context.client.connection)
                 try:
                     if sub_folder.lock:
                         folder_api.auth(sub_folder.id, context.password)
                     folder = folder_api.retrieve(sub_folder.id)
-                    files = cls._find_files(context.connection, sub_folder.id)
+                    files = context.client.find_files(sub_folder.id)
                     cls._ls_plain(context, folder, files)
                 except UnauthorizedException:
                     pass
@@ -174,7 +180,7 @@ class LsCommand(BaseCommand):
             "updated_at": folder.updated_at,
         }
         if isinstance(folder, Folder):
-            folder_api = FoldersApi(context.connection)
+            folder_api = FoldersApi(context.client.connection)
             data["metadata"] = folder_api.metadata(folder.id)
             if context.is_recursive:
                 sub_folders: list[dict[str, Any]] = []
@@ -183,7 +189,7 @@ class LsCommand(BaseCommand):
                         if sub_folder.lock:
                             folder_api.auth(sub_folder.id, context.password)
                         folder2 = folder_api.retrieve(sub_folder.id)
-                        files2 = cls._find_files(context.connection, sub_folder.id)
+                        files2 = context.client.find_files(sub_folder.id)
                         sub_folders.append(cls._folder2dict(context, folder2, files2))
                     except UnauthorizedException:
                         pass
@@ -205,7 +211,7 @@ class LsCommand(BaseCommand):
             # "thumbnail": file.thumbnail,
             "description": file.description,
             "metadata": file.metadata,
-            "download_url": f"{context.connection.url}/{file.download_url}",
+            "download_url": f"{context.client.connection.url}/{file.download_url}",
             "created_at": file.created_at,
             "updated_at": file.updated_at,
         }
@@ -213,5 +219,5 @@ class LsCommand(BaseCommand):
 
     @classmethod
     def _laboratory_name(cls, context: LsCommandContext, laboratory_id: int) -> str:
-        laboratory = context.connection.laboratories.find_by_id(laboratory_id)
+        laboratory = context.client.connection.laboratories.find_by_id(laboratory_id)
         return laboratory.name if laboratory is not None else "(invalid)"